Multiple platform build/check report for BioC 3.11 - BUILD report for mCSEA on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data mCSEA
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* checking for file ‘mCSEA/DESCRIPTION’ ... OK
* preparing ‘mCSEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘mCSEA.Rmd’ using rmarkdown
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: mCSEAdata
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'mCSEA'

The following object is masked from 'package:mCSEAdata':

    exprTest

[estimateCellCounts] Combining user data with reference (flow sorted) data.

[estimateCellCounts] Processing user and reference data together.

[preprocessQuantile] Mapping to genome.
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
[preprocessQuantile] Fixing outliers.
[preprocessQuantile] Quantile normalizing.
[estimateCellCounts] Picking probes for composition estimation.

[estimateCellCounts] Estimating composition.

Warning in fgsea::fgsea(genes, rank, minSize = minCpGs, nperm = nperm, nproc = nproc) :
  You are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument in the fgsea function call.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam) :
  There are ties in the preranked stats (7.59% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam) :
  There are duplicate gene names, fgsea may produce unexpected results.
[WARNING] Could not parse YAML metadata at line 100 column 1: :31:71: Unexpected '
  '
pandoc-citeproc: reference mcgregor16 not found
pandoc-citeproc: reference mcgregor16 not found
pandoc-citeproc: reference du10 not found
pandoc-citeproc: reference jones12 not found
pandoc-citeproc: reference jones12 not found
! Undefined control sequence.
l.76 \definecolor
                 {fgcolor}{rgb}{0.251, 0.251, 0.251} 

Error: processing vignette 'mCSEA.Rmd' failed with diagnostics:
LaTeX failed to compile mCSEA.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See mCSEA.log for more info.
--- failed re-building ‘mCSEA.Rmd’

SUMMARY: processing the following file failed:
  ‘mCSEA.Rmd’

Error: Vignette re-building failed.
Execution halted
BUILD report for mCSEA on celaya2

Summary

Command output
